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Receptor
PDB id Resolution Class Description Source Keywords
1GAR 1.96 Å EC: 2.1.2.2 TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE R IBONUCLEOTIDE TRANSFORMYLASE AT 1.96 ANGSTROMS RESOLUTION ESCHERICHIA COLI TRANSFERASE (FORMYL)
Ref.: TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT 1.96 A RESOLUTION. J.MOL.BIOL. V. 249 153 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U89 A:213;
B:213;
Valid;
Valid;
none;
none;
Ki = 100 pM
715.669 C27 H38 N7 O12 P S c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1GAR 1.96 Å EC: 2.1.2.2 TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE R IBONUCLEOTIDE TRANSFORMYLASE AT 1.96 ANGSTROMS RESOLUTION ESCHERICHIA COLI TRANSFERASE (FORMYL)
Ref.: TOWARDS STRUCTURE-BASED DRUG DESIGN: CRYSTAL STRUCTURE OF A MULTISUBSTRATE ADDUCT COMPLEX OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AT 1.96 A RESOLUTION. J.MOL.BIOL. V. 249 153 1995
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1GAR Ki = 100 pM U89 C27 H38 N7 O12 P S c1cc(ccc1C....
2 1JKX Ki = 20 uM 138 C30 H37 N6 O15 P c1cc(ccc1C....
3 1C3E - NHR C23 H22 N4 O8 c1cc(ccc1[....
4 1CDE - GAR C7 H13 N2 O8 P C([C@@H]1[....
5 1C2T Ki = 260 nM NHS C23 H22 N4 O8 c1cc(ccc1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1GAR Ki = 100 pM U89 C27 H38 N7 O12 P S c1cc(ccc1C....
2 1JKX Ki = 20 uM 138 C30 H37 N6 O15 P c1cc(ccc1C....
3 1C3E - NHR C23 H22 N4 O8 c1cc(ccc1[....
4 1CDE - GAR C7 H13 N2 O8 P C([C@@H]1[....
5 1C2T Ki = 260 nM NHS C23 H22 N4 O8 c1cc(ccc1[....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4ZYY Ki = 9 nM 3YC C20 H23 N5 O6 S c1c(csc1CC....
2 4ZYU Ki = 1067 nM 3YA C22 H24 N4 O6 S c1cc(ccc1C....
3 4ZZ1 Ki = 13 nM 3YF C19 H21 N5 O6 S c1c(csc1C(....
4 1RBM Ki = 4 nM KT5 C42 H54 F3 N9 O20 c1cc(ccc1[....
5 1RBQ - KEU C22 H30 F3 N5 O8 c1cc(ccc1[....
6 4EW3 Ki = 0.18 uM DXZ C21 H27 N5 O6 S CS[C@H](CC....
7 4EW2 - DXY C21 H27 N5 O6 S CS[C@@H](C....
8 4ZYT Ki = 17 nM 3Y9 C22 H25 N5 O6 c1cc(ccc1C....
9 1RC1 - KT3 C32 H40 F3 N7 O14 c1cc(ccc1[....
10 1RBY - KEU C22 H30 F3 N5 O8 c1cc(ccc1[....
11 4ZYW Ki = 68 nM G94 C19 H21 N5 O6 S c1cc(sc1CC....
12 4ZZ3 Ki = 1000 nM 4DW C20 H19 N5 O6 c1cc(ccc1C....
13 4ZYZ Ki = 67 nM 3YD C18 H25 N5 O6 c1c([nH]c2....
14 1MEN - GAR C7 H13 N2 O8 P C([C@@H]1[....
15 1RC0 Ki = 4 nM KT5 C42 H54 F3 N9 O20 c1cc(ccc1[....
16 4ZYX Ki = 7 nM 3YB C20 H23 N5 O6 S c1c(csc1C(....
17 4ZZ0 Ki = 99 nM 3YE C19 H27 N5 O6 c1c([nH]c2....
18 4ZZ2 Ki = 9.1 nM 3YG C19 H21 N5 O6 S c1c(csc1CC....
19 1ZLY - GRF C5 H12 N O7 P C([C@@H]1[....
20 5J9F Ki = 59 nM 83A C20 H22 N6 O6 c1cc(ccc1C....
21 1NJS Ki = 15 nM KEU C22 H30 F3 N5 O8 c1cc(ccc1[....
22 1RBZ Ki = 4 nM KT5 C42 H54 F3 N9 O20 c1cc(ccc1[....
23 4ZYV Ki = 22 nM G71 C20 H23 N5 O6 S c1cc(sc1CC....
24 1GAR Ki = 100 pM U89 C27 H38 N7 O12 P S c1cc(ccc1C....
25 1JKX Ki = 20 uM 138 C30 H37 N6 O15 P c1cc(ccc1C....
26 1C3E - NHR C23 H22 N4 O8 c1cc(ccc1[....
27 1CDE - GAR C7 H13 N2 O8 P C([C@@H]1[....
28 1C2T Ki = 260 nM NHS C23 H22 N4 O8 c1cc(ccc1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U89; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 U89 1 1
2 DXZ 0.487805 0.722892
3 DXY 0.487805 0.722892
4 9L9 0.406504 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1GAR; Ligand: U89; Similar sites found with APoc: 148
This union binding pocket(no: 1) in the query (biounit: 1gar.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 2OFD NGA None
2 2UYN 2KT None
3 1F28 UMP 0.943396
4 1ZD9 GDP 1.06383
5 1Y2W NAG 1.40845
6 3B5J 12D 1.88679
7 4G9N NGA 2.0979
8 1GXU 2HP 2.1978
9 5GVR LMR 2.35849
10 3HKW IX6 2.35849
11 1GOJ ADP 2.35849
12 3O5N BR0 2.67857
13 5JQ1 ZPF 2.75862
14 5E5U MLI 2.83019
15 4WZ6 ATP 2.83019
16 2Z9I GLY ALA THR VAL 2.83019
17 2OBM ADP 2.83019
18 3THR C2F 2.83019
19 4DFU QUE 2.83019
20 2Y65 ADP 2.83019
21 3B7G ANP 2.83019
22 3R4S SIA 2.83019
23 6FA4 GNP 2.89017
24 1TLG GAL 3.2
25 1Q19 SSC 3.30189
26 5TSH ADP 3.30189
27 2AAZ UMP 3.30189
28 4ZNO SUC 3.30189
29 6M7X JD7 3.30189
30 3A4M ADP 3.30189
31 2BQP GLC 3.30189
32 3QDW A2G 3.4965
33 3QDV A2G 3.4965
34 3QDY A2G GAL 3.4965
35 3QDT A2G GAL 3.4965
36 3QDX A2G GAL 3.4965
37 1CBK ROI 3.75
38 5NM7 GLY 3.7594
39 2OG2 MLI 3.77358
40 3TY3 GGG 3.77358
41 1G8S MET 3.77358
42 3B9Q MLI 3.77358
43 4B2D SER 3.77358
44 1J3I UMP 3.77358
45 3DRW AMP 3.77358
46 2CBZ ATP 3.79747
47 2F5X ASP 3.84615
48 2C3H GLC GLC 4.08163
49 5WXU FLC 4.24528
50 1DLL LAT 4.24528
51 2GK6 ADP 4.24528
52 4ZUL UN1 4.71698
53 2RI1 GLP 4.71698
54 2DVZ GLU 4.71698
55 1SL6 GAL NDG FUC 4.8913
56 2G77 AF3 5.05051
57 5AHN IMP 5.18868
58 5EYW PGA 5.18868
59 2Q8M AMP 5.18868
60 4CVN ADP 5.2356
61 4NAE 1GP 5.66038
62 5WJ6 B4A 5.66038
63 4U00 ADP 5.66038
64 2VVG ADP 5.66038
65 4WQQ MAN 5.67376
66 5FII PHE 5.88235
67 2X7I CIT 6.13208
68 1R0X ATP 6.13208
69 2D2F ADP 6.13208
70 2PZE ATP 6.13208
71 4EIL UMP 6.13208
72 2FR6 URI 6.16438
73 2FR6 CTN 6.16438
74 3KUD GDP 6.17284
75 2X2T GAL NGA 6.53595
76 1B0U ATP 6.60377
77 1NE7 16G 6.60377
78 1KNM LAT 6.92308
79 2WPB ZZI 7.07547
80 1G6H ADP 7.07547
81 5YV5 ADP 7.07547
82 1YQT ADP 7.07547
83 3KC1 2T6 7.07547
84 5C79 PBU 7.33333
85 5MQW GTP 7.54717
86 5MQW ATP 7.54717
87 2AWN ADP 7.54717
88 5T63 ALA ALA ALA ALA 7.54717
89 3COB ADP 7.54717
90 5MUA GAL 7.54717
91 3RKR NAP 7.54717
92 4N14 WR7 8.01887
93 3NZ1 3NY 8.01887
94 4C2C ALA ALA ALA 8.49057
95 1XVB BHL BHL 8.49057
96 4AG5 ADP 8.96226
97 1XX6 ADP 9.42408
98 6CAM BGC 9.43396
99 1GJW GLC 9.43396
100 2KIN ADP 9.43396
101 2A9W UMP 9.90566
102 1ZPR UMP 9.90566
103 6CDZ UMP 9.90566
104 1JG0 UMP 9.90566
105 1TSD UMP 9.90566
106 1DDU DDU 9.90566
107 1AIQ UMP 9.90566
108 1TLC DGP 9.90566
109 4ISK UMP 9.90566
110 6CDZ UMC 9.90566
111 4LO2 GAL BGC 9.90566
112 1SYN UMP 9.90566
113 1NCE UMP 9.90566
114 5ZXD ATP 9.90566
115 1AXW UMP 9.90566
116 3FGZ BEF 10.1562
117 3ITJ CIT 10.3774
118 1RRC ADP 10.3774
119 3K0T BGC 10.4895
120 4IF4 BEF 10.5769
121 2W58 ADP 11.8812
122 2VMG MBG 12.1019
123 1JJ7 ADP 12.2642
124 2NU8 COA 12.2642
125 2QQD AG2 12.5
126 3K5I AIR 12.7358
127 3W9F I3P 12.7358
128 5O96 SAM 12.7358
129 2ZQO NGA 14.6154
130 4PPF FLC 15.566
131 4TTS 6DD 16.5094
132 4LXQ TYD 16.9811
133 4LXQ FON 16.9811
134 5VYQ FON 18.3962
135 5UWQ GNP 18.3962
136 4XCZ FON 18.8679
137 4XCZ T3Q 18.8679
138 6EDK 1YA 19.3396
139 2BLN FON 20.283
140 2BLN U5P 20.283
141 5UIJ TYD 21.2264
142 5VYR B62 21.6981
143 5VYR GMP 21.6981
144 4YFY 1YJ 22.1698
145 5OM2 DXT 22.5
146 1FQJ ALF 26.1905
147 1LOJ URI 28.7356
148 2CFI ZZZ 31.1321
Pocket No.: 2; Query (leader) PDB : 1GAR; Ligand: U89; Similar sites found with APoc: 34
This union binding pocket(no: 2) in the query (biounit: 1gar.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC NBU None
2 4Z2S NAG None
3 4Z2S NDG None
4 1JJV ATP 0.970874
5 1UPF URF 1.88679
6 5NC9 8SZ 2.35849
7 5N1P 8GK 2.42718
8 1SQL GUN 2.73973
9 5BSH PRO 2.83019
10 1B5E DCM 2.83019
11 3NBC LAT 3.37838
12 1YQC GLV 3.52941
13 3MWL 8OX 3.86473
14 5A96 GTP 4.24528
15 2B6N ALA PRO THR 4.24528
16 1B09 PC 4.36893
17 1XTT U5P 4.71698
18 6C0B MLI 4.71698
19 3AIA SAM 4.73934
20 1ONI BEZ 5.07246
21 2GKS ADP 5.18868
22 1JI0 ATP 5.66038
23 5N6N SUC 5.66038
24 3TD3 GLY 5.69106
25 2F6U CIT 7.07547
26 1WTC ACP 7.54717
27 3F9W SAH 7.83133
28 2R68 SUP 8.01887
29 1O5O U5P 8.96226
30 4OUJ LBT 9.43396
31 5FJJ MAN 10.8491
32 6GPC ARG 11.1111
33 4LSY FLC 19.7802
34 1LOJ U 28.7356
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